Bayern lost the semi-final first leg 1-0 in Spain, but won the return 2-1 in Munich on Tuesday as Atletico Madrid triumphed on away goals.
Antoine Griezmann's crucial goal for Atletico made all the difference at the Allianz Arena as the tie finished 2-2 on aggregate.
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Xabi Alonso and Robert Lewandowski netted for Bayern on a night when both teams missed penalties in Munich.
Bayern have again exited the semi-finals in Europe to Spanish opponents after losing to Barcelona in 2015 and were also dumped out of the last four by Real Madrid in 2014.
Guardiola was asked if he viewed his time in Munich as a failure despite winning five trophies so far, including two German league titles. "Yes, in terms of what we have won," he replied.
"It was my goal to win the Champions League final with Bayern after doing it with Barcelona (in 2009 and 2011).
"Perhaps we have helped the players, maybe it's not enough, but it was the important thing for me.
"I've given my life for this club, I've fought and done my best, the people can say what they want, but it was really an honour to work with these players."
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Bayern can become the first team to win four consecutive German league titles if they beat Ingolstadt on Saturday and then face Borussia Dortmund in the German Cup final on May 21.
But Guardiola, who will coach Manchester City next season, says the chance to win the double does not make up for the disappointment of another semi-final exit.
He hopes his replacement, Carlo Ancelotti, can now win the European title next season with Bayern.
"Of course we want to win the German Cup, we also want to win the league, but it won't change my opinion of my time here by winning the cup," said Guardiola.
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"Titles are numbers, statistics are statistics.
"I wanted to reach the (Champions League) final, I haven't managed it, I hope Carlo can do it next season.
"We haven't managed it, we're sad, but we have to prepare for the league game at Ingolstadt."
Guardiola said he had no regrets in his team selection having recalled Thomas Mueller, Franck Ribery and Jerome Boateng in three changes from the side which lost the first leg.
"You are disappointed when you dont play well. When you go home feeling you have not given all. Today I dont feel like that," he said.
"We just didn't achieve our goals.
"We tried our best, but I don't have the feeling we let the fans down.
"We prepared well, but Atletico deserve to reach the final."
Bayern captain Philipp Lahm said the squad regretted failing to reach the European final in Guardiola's swansong season.
"The team isn't to blame, we tried everything, but unfortunately it wasn't enough," said Lahm.
"We failed to get the goals at the right time.
"It's a bitter result that we haven't been able to reward ourselves and the coaching staff for the work over the last three years."
Having missed his first-half penalty, Mueller was left to rue the chances that got away.
"Football is sometimes so extreme," said the 26-year-old.
"We did a lot right and only a few things wrong, unfortunately it wasn't enough.
"I haven't experienced many nights like this here, the sting goes very deep.
"Of course, I am disappointed not to have converted the penalty."
Goal-scorer Robert Lewandowski admitted it was hard to bow out having won in Munich.
"It's hard to accept, because we had deserved the win," said Lewandowski after Bayern failed to score a crucial third goal.
"To go out like that hurts."
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